Since 2006, hundreds of people have reportedly been abducted by the security forces or armed groups in areas in the north and east of Sri Lanka, as well as in Colombo, the London-based rights group said.
In a report marking the International Day of the Disappeared, which falls on August 30, Amnesty said many people taken in for questioning had subsequently disappeared.
It said the Vice-Chancellor of Eastern University, Sivasubramanium Raveendranath, was reportedly abducted while at a conference in Colombo in December and his whereabouts were unknown.
"He was in an area of the capital tightly controlled by the army.
It is likely that his captors were military agents," Amnesty said.
"He has not been heard from since.
"
"There are currently 5,749 outstanding cases of enforced disappearance in Sri Lanka being reviewed by the UN Working Group on Enforced or Involuntary Disappearances," the rights group added.
There was no immediate comment from the government about the latest